Energetic and structural properties of complexes formed from interaction between selenium analog of methimazole (MSeI) as an anti-thyroid drug and Mz+ (Li+, Na+, K+, Be2+, Mg2+ and Ca2+) cations have been investigated using B3LYP, M062X, PBE1PBE, and MP2 methods with 6-311++G(d,p) and 6-311++G(2d,2p) basis sets. Two planar and perpendicular complexes were predicted from interaction of MSeI and Mz+ cations. From the Gibbs free energy difference between the planar and perpendicular forms of MSeI–Mz+ complexes, it is found that the perpendicular forms are the predominant ones. In addition, the comparison of interaction energies shows that the order of energies increases in the following order: K+ < Na+ < Li+ < Ca2+ < Mg2+ < Be2+. The results of natural bond orbital analysis showed that the charge transfer occurs from MSeI to metal cations. The atom in molecule analysis shows that the charge density and its Laplacian at the Se–Mz+ bond critical point of the MSeI–M2+ complexes are greater than the MSeI–M1+ ones. Also, it was revealed that the Se–Mz+ interactions in perpendicular complexes of alkali and alkaline metal cations are electrostatic and partially covalent in nature, respectively.